Changeset 3212

Timestamp:

May 5, 2014, 9:00:56 AM (9 years ago)

Author:

Peter

Message:

move Cigar defines to a separate file

Location:

trunk/yat

Files:

• omic/BamRead.h (modified) (3 diffs)
• utility/Aligner.cc (modified) (1 diff)
• utility/Aligner.h (modified) (1 diff)
• utility/Cigar.h (added)
• utility/Makefile.am (modified) (1 diff)
• utility/SmithWaterman.cc (modified) (1 diff)

trunk/yat/omic/BamRead.h

@@ -23 +23 @@
 */
 
-#include <yat/utility/config_public.h>
-
-// allow inclusion of config_bam.h so this file is available also without bam.h
-#ifdef YAT_HAVE_LIBBAM
 #include "config_bam.h"
 #include YAT_BAM_HEADER
 #include YAT_SAM_HEADER
 
-#else
-/// describe how CIGAR operation/length is packed into a 32-bit
-#define BAM_CIGAR_SHIFT 4
-/// operation is described in four lowest bits
-#define BAM_CIGAR_MASK  ((1 << BAM_CIGAR_SHIFT) - 1)
-/// \abstract CIGAR: M = match or mismatch
-#define BAM_CMATCH      0
-/// \abstract CIGAR: I = insertion to the reference
-#define BAM_CINS        1
-/// \abstract CIGAR: D = deletion from the reference
-#define BAM_CDEL        2
-/// \abstract CIGAR: N = skip on the reference (e.g. spliced alignment)
-#define BAM_CREF_SKIP   3
-/// \abstract CIGAR: S = clip on the read with clipped sequence
-/// present in qseq
-#define BAM_CSOFT_CLIP  4
-/// \abstract CIGAR: H = clip on the read with clipped sequence trimmed off
-#define BAM_CHARD_CLIP  5
-/// \abstract CIGAR: P = padding
-#define BAM_CPAD        6
-/// \abstract CIGAR: equals = match
-#define BAM_CEQUAL      7
-/// \abstract CIGAR: X = mismatch
-#define BAM_CDIFF       8
-#define BAM_CBACK       9
-#endif
+// This file has to be included to keep compatibility with yat 0.11
+#include <yat/utility/Cigar.h>
 
 #include <functional>
@@ -62 +34 @@
 #include <vector>
 
-// backport #defines from samtools 0.1.19
-#ifndef BAM_CIGAR_STR
-#define BAM_CIGAR_STR "MIDNSHP=XB"
-// lookup table used in bam_cigar_type
-#define BAM_CIGAR_TYPE 0x3C1A7
-
-/// index of operation in range [0, 9], see below.
-#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
-// length of the operation
-#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
-// char describing the operation, see column 2 in table below
-#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
-// Create a cigar element with length l and operation o
-#define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))
-// Returns a two-bits number describing the type of operation. The
-// first bit, bam_cigar_type & 1, (4th column in table below) is 1 iff
-// operation consumes query sequence. The second bit, bam_cigar_type &
-// 2, (3rd column below) is 1 iff operation consumes reference
-// sequence.
-#define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3)
-#endif
-
-/*
-  CIGAR
-0 M 1 1 match
-1 I 0 1 insert
-2 D 1 0 deletion
-3 N 1 0 spliced (rna)
-4 S 0 1 soft clipped
-5 H 0 0 hard clipped
-6 P 0 0 padded
-7 = 1 1 equal
-8 X 1 1 mismatch
-9 B 0 0
-
-3rd column: consumes reference sequence
-4th column: consumes query sequence
- */
-
-#ifdef YAT_HAVE_LIBBAM
 namespace theplu {
 namespace yat {
@@ -457 +389 @@
 }}}
 #endif
-#endif

trunk/yat/utility/Aligner.cc

@@ -23 +23 @@
 
 #include "Aligner.h"
+#include "Cigar.h"
 #include "Matrix.h"
-
-// to get BAM_CIGAR defines
-#include <yat/omic/BamRead.h>
 
 #include <cassert>

trunk/yat/utility/Aligner.h

@@ -172 +172 @@
 
        \since new in yat 0.12
+
+       \see file yat/utility/Cigar.h for some useful macros
      */
     class Cigar

trunk/yat/utility/Makefile.am

@@ -61 +61 @@
   $(srcdir)/yat/utility/Alignment.h \
   $(srcdir)/yat/utility/boost_exception_ptr.h \
+  $(srcdir)/yat/utility/Cigar.h \
   $(srcdir)/yat/utility/ColumnStream.h \
   $(srcdir)/yat/utility/CommandLine.h \

trunk/yat/utility/SmithWaterman.cc

@@ -23 +23 @@
 
 #include "SmithWaterman.h"
-#include "yat/omic/BamRead.h" // for cigar defines
+#include "Cigar.h"
 
 #include <cassert>